Merge pull request #19 from ScilifelabDataCentre/fresh_rebuild

Project rebuild in fresh branch

.flaskenv

@@ -0,0 +1,2 @@
+FLASK_APP=app
+FLASK_DEBUG=1

.gitignore

@@ -66,7 +66,7 @@ db.sqlite3
 db.sqlite3-journal
 
 # Flask stuff:
-instance/
+#instance/
 .webassets-cache
 
 # Scrapy stuff:
@@ -157,4 +157,4 @@ dmypy.json
 cython_debug/
 
 # Project specific
-.flaskenv
+#.flaskenv

Dockerfile

@@ -1,9 +1,7 @@
-FROM python:3.11.0
-
-WORKDIR .
-
-COPY . .
-
+FROM python:3.11
+EXPOSE 5000
+WORKDIR /app
+COPY requirements.txt .
 RUN pip install -r requirements.txt
-
-CMD ["python3", "run.py"]
+COPY . .
+CMD ["flask", "run", "--host", "0.0.0.0"]

app.py

@@ -0,0 +1,30 @@
+import os
+
+from flask import Flask
+from flask_smorest import Api
+from flask_migrate import Migrate
+
+from db import db
+
+from resources.articles import blp as ArticleBlueprint
+
+def create_app(db_url=None):
+    app = Flask(__name__)
+
+    app.config["PROPAGATE_EXCEPTIONS"] = True
+    app.config["API_TITLE"] = "Precision Medicine Portal REST API"
+    app.config["API_VERSION"] = "v1"
+    app.config["OPENAPI_VERSION"] = "3.0.3"
+    app.config["OPENAPI_URL_PREFIX"] = "/"
+    app.config["OPENAPI_SWAGGER_UI_PATH"] = "/swagger-ui"
+    app.config["OPENAPI_SWAGGER_UI_URL"] = "https://cdn.jsdelivr.net/npm/swagger-ui-dist/"
+    app.config["SQLALCHEMY_DATABASE_URI"] = db_url or os.getenv("DATABASE_URL", "sqlite:///data.db")
+    app.config["SQLALCHEMY_TRACK_MODIFICATIONS"] = False
+
+    db.init_app(app)
+    migrate = Migrate(app, db)
+    api = Api(app)
+
+    api.register_blueprint(ArticleBlueprint)
+
+    return app

db.py

@@ -0,0 +1,3 @@
+from flask_sqlalchemy import SQLAlchemy
+
+db = SQLAlchemy()

migrations/README

@@ -0,0 +1 @@
+Single-database configuration for Flask.

migrations/alembic.ini

@@ -0,0 +1,50 @@
+# A generic, single database configuration.
+
+[alembic]
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic,flask_migrate
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[logger_flask_migrate]
+level = INFO
+handlers =
+qualname = flask_migrate
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

migrations/env.py

@@ -0,0 +1,113 @@
+import logging
+from logging.config import fileConfig
+
+from flask import current_app
+
+from alembic import context
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+logger = logging.getLogger('alembic.env')
+
+
+def get_engine():
+    try:
+        # this works with Flask-SQLAlchemy<3 and Alchemical
+        return current_app.extensions['migrate'].db.get_engine()
+    except (TypeError, AttributeError):
+        # this works with Flask-SQLAlchemy>=3
+        return current_app.extensions['migrate'].db.engine
+
+
+def get_engine_url():
+    try:
+        return get_engine().url.render_as_string(hide_password=False).replace(
+            '%', '%%')
+    except AttributeError:
+        return str(get_engine().url).replace('%', '%%')
+
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+config.set_main_option('sqlalchemy.url', get_engine_url())
+target_db = current_app.extensions['migrate'].db
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+
+def get_metadata():
+    if hasattr(target_db, 'metadatas'):
+        return target_db.metadatas[None]
+    return target_db.metadata
+
+
+def run_migrations_offline():
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url, target_metadata=get_metadata(), literal_binds=True
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online():
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+
+    # this callback is used to prevent an auto-migration from being generated
+    # when there are no changes to the schema
+    # reference: http://alembic.zzzcomputing.com/en/latest/cookbook.html
+    def process_revision_directives(context, revision, directives):
+        if getattr(config.cmd_opts, 'autogenerate', False):
+            script = directives[0]
+            if script.upgrade_ops.is_empty():
+                directives[:] = []
+                logger.info('No changes in schema detected.')
+
+    conf_args = current_app.extensions['migrate'].configure_args
+    if conf_args.get("process_revision_directives") is None:
+        conf_args["process_revision_directives"] = process_revision_directives
+
+    connectable = get_engine()
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection,
+            target_metadata=get_metadata(),
+            **conf_args
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

migrations/script.py.mako

@@ -0,0 +1,24 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision = ${repr(up_revision)}
+down_revision = ${repr(down_revision)}
+branch_labels = ${repr(branch_labels)}
+depends_on = ${repr(depends_on)}
+
+
+def upgrade():
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade():
+    ${downgrades if downgrades else "pass"}

migrations/versions/2e31a9fa93ae_.py

@@ -0,0 +1,35 @@
+"""empty message
+
+Revision ID: 2e31a9fa93ae
+Revises: 
+Create Date: 2024-04-04 20:55:16.111285
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '2e31a9fa93ae'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('articles',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('title', sa.String(length=80), nullable=False),
+    sa.Column('url_str', sa.String(length=80), nullable=False),
+    sa.Column('is_available', sa.Boolean(), nullable=False),
+    sa.Column('markdown_text', sa.String(), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('articles')
+    # ### end Alembic commands ###

models/__init__.py

@@ -0,0 +1 @@
+from models.article import ArticleModel

models/article.py

@@ -0,0 +1,14 @@
+from db import db
+
+class ArticleModel(db.Model):
+    """
+    Article is a piece of content that will be in markdown format together with this
+    database class that will include meta-data, including the link to the content in storage.
+    """
+    __tablename__ = 'articles'
+
+    id = db.Column(db.Integer, primary_key=True)
+    title = db.Column(db.String(80), nullable = False)
+    url_str = db.Column(db.String(80), nullable = False, default="article_"+id)
+    is_available = db.Column(db.Boolean, nullable = False, default=False)
+    markdown_text = db.Column(db.String, nullable = False)

requirements.txt

@@ -1,13 +1,6 @@
-blinker==1.7.0
-click==8.1.7
-Flask==3.0.0
-importlib-metadata==6.8.0
-itsdangerous==2.1.2
-Jinja2==3.1.2
-jsonify==0.5
-Markdown==3.5.1
-MarkupSafe==2.1.3
-python-dotenv==1.0.0
-shortuuid==1.0.11
-Werkzeug==3.0.1
-zipp==3.17.0
+flask
+flask-smorest
+python-dotenv
+sqlalchemy
+flask-sqlalchemy
+flask-migrate